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GeVarLi : GEnome assembly, VARiant calling and LIneage assignation. https://transvihmi.pages.ird.fr/nfernandez/GeVarLi/en

dojo snakemake assemblage long reads

Are you looking for a simplified installation process for your Snakemake workflows, including the various Python packages and the multitude of tools used by your pipelines?

Would you like to simplify the use of your workflows with user-friendly commands and subcommands that even non-bioinformatician users can easy use? Look no further - Snakecdysis is the solution for you!

This pipeline is an automatic structural annotation workflows written in snakemake. The annotation is based on two tools which uses RNA-Seq and/or protein homology information for predict coding sequence. One of this tools is BRAKER which use GeneMark-EX and AUGUSTUS. And the other tool is AUGUSTUS alone for improve annotation of small coding sequences with few or no intron. Before the annotation, the repeat element of genome are masked for avoid annotation probleme. In addition this workflows can perform a illumina assembly with ABySS using différent value of kmere.

snakemake workflow for mappind single/paired datas

Reads Quality Control (RQC) allow raw NGS reads quality control, before continue with more downstream analysis.

Git : l'outil incontournable pour la gestion et le contrôle de version de vos fichiers https://isi.pages.ird.fr/isi-formation-git/

GraTools is a powerful tool for analyzing and handling pangenome graphs quickly, whatever the model' and therefore the size and the complexity of the GFA file. It allows users to extract sequences or subgraphs, convert graphs into FASTA sequences, and identify shared and specific nodes across samples. Additionally, it provides essential statistics for chromosomes and samples data. With multi-threading support and flexible logging capabilities, Gratools is an efficient solution for pangenome graph analysis.

Materials for Learning Bioinformatics and Enhancing Competencies - Conda https://mivegec.pages.ird.fr/dainat/malbec-conda/

Install Conda using Miniforge3 script

Materials for Learning Bioinformatics and Enhancing Competencies - Containers https://mivegec.pages.ird.fr/dainat/malbec-containers/

SLURM Lightweight Automated Manager

https://doc-forge.pages.ird.fr